Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatttatctttctctaaggatgtatttgtctgtgtacactatttgatgtttgagaacaagcttattttctctctgagaatcgtttcttaaaatgggaatagcaagattgctaaaatctttaatgtttcttgtgtaagGAGCAAGAGGTGGTTCTGAGGTCTATGCCAGATATTGTTGTGGCGACTCCTGGACGTATGATAGATCATTTGCGTAATTCTATGTCTGTTGATTTGGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16630.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16630.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G11950.1 (Glycine max), 3'ss of exon 5
gtatgtatttatctttctctaaggatgtatttgtctgtgtacactatttgatgtttgagaacaagcttattttctctctgagaatcgtttcttaaaatgggaatagcaagattgctaaaatctttaatgtttcttgtgtaagGAGCAAGAGGTGGTTCTGAGGTCTATGCCAGATATTGTTGTGGCGACTCCTGGACGTATGATAGATCATTTGCGTAATTCTATGTCTGTTGATTTGGATG
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----------------------------------caatgtg-gcttttacagctttaaaaatt--cccactattatctagttgattgcaccctt---tgctatttatttattctttaaaaaaggtgtt--ttctcatcctagGTGCAAGAGGCTGCTTTGAGAACAATGCCAGACATTGTTGTGGCTACTCCAGGACGCATGATAGACCATTTACGCAATGCTATGTCCGTGGATTTGGATG
upper sequence: AT4G16630.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G25240.1 (Glycine max), 3'ss of exon 5
gtatgtatttatctttctctaaggatgtatttgtctgtgtacactatttgatgtttgagaacaagcttattttctctctgagaatcgtttcttaaaatgggaatagcaagattgctaaaatctttaatgtttcttgtgtaagGAGCAAGAGGTGGTTCTGAGGTCTATGCCAGATATTGTTGTGGCGACTCCTGGACGTATGATAGATCATTTGCGTAATTCTATGTCTGTTGATTTGGATG
| ||| || | | || | ||| | || | ||| ||| ||| | | || || || ||| ||| | ||||| | ||| |||||||| | | |||| | |||||||| ||||||||||| ||||| ||||| |||||||| ||||| || ||| ||||||| || ||||||||||
-----------------tttaaaaattcccactattatcta-gttgattggtaacgcaggtaatgctgattgcctcctttaatatttattgtttaaa----aatggtgt--------------------tttctcatcctagGTGCAAGAGGCTGCTTTGAGAACAATGCCAGACATTGTTGTGGCTACTCCAGGACGCATGATAGACCATTTACGCAATGCTATGTCCGTGGATTTGGATG
upper sequence: AT4G16630.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv18s0001g14540.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtatttatctttctctaaggatgtatttgtctgtgtacactatttgatgtttgagaacaagcttattttctctctgagaatcgtttcttaaaatgggaatagcaagattgctaaaatctttaatgtttcttgtgtaagGAGCAAGAGGTGGTTCTGAGGTCTATGCCAGATATTGTTGTGGCGACTCCTGGACGTATGATAGATCATTTGCGTAATTCTATGTCTGTTGATTTGGATG
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----------------------------tttattttgaaagtgttgattgcctcttcatcatataattaacctttttacttgttttgtttgc----atcaaaattgttatggtgatggcacatttacttt----------agATGCAAGAGACAGCTTTGAGATCAATGCCTGATGTTGTTGTGGCTACCCCGGGACGGATGATAGATCATTTACGCAATTCCATGTCTGTGGATTTGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcttaaaatgggaatagcaagattgctaaaatctttaatgtttcttgtgtaagGAGCAAGAGGTGGTTCTGAGGTCTATGCCAGATATTGTTGTGGCGACTCCTGGACGTATGATAGATCATTTGCGTAATTCTATGTCTGTTGATTTGGATG
tgtttctt CT-rich tract
taaaatctttaatgtt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatttatctttctctaaggatgtatttgtctgtgtacactatttgatgtttgagaacaagcttattttctctctgagaatcgtttcttaaaatgggaatagcaagattgctaaaatctttaatgtttcttgtgtaagGAGCAAGAGGTGGTTCTGAGGTCTATGCCAGATATTGTTGTGGCGACTCCTGGACGTATGATAGATCATTTGCGTAATTCTATGTCTGTTGATTTGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA